Derek,Homeobox genes, their distribution, and apparent conservation are an interesting discovery of the last few decades. However, we've known about homology since pre-Darwinian times. Moreover, the importance of homeobox genes and their apparent conservation lies in how their expression maps to features we already know to be homologous (i.e. head, thorax, wings legs, etc.).

I agree. But the point is that Darwin made successful use of the concept of homology, as did many scientists before him. Darwin distinguished himself from previous workers in being able to explain homology in terms of common ancestry. He was able to do this long before we knew anything about genes, let alone gene expression patterns in embryos.

Today, gene expression patterns (as well as other developmental criteria) have become "big business" in terms of the resolution of homology. My question remains the same: do they act as a guide and, if so, what is the theoretical justification for this conclusion? If they don't act as a guide, why not and how do we know?

I thought cause and effect has been demonstrated clearly. E.g., removing the "eye" gene produces flies with no eyes, or putting the eye gene in different locations will create flies with eyes on different parts of the body. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HomeoboxGenes.html

Anyways, homology isn't needed for genetics anymore, there are other things, like protein/enzyme structure and mitochondrial DNA that can be used to show hereditary relationships.

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Research Fellow at NCB Naturalis in Leiden, the Netherlands. My research interests include the fossil record and early evolutionary history of jawed vertebrates. The opinions expressed on this blog are my own and do not necessarily reflect those of NCB Naturalis.